We investigate the propagation of Alfven waves in the solar chromosphere, distinguishing between upward and downward propagating waves. We find clear evidence for the reflection of waves in the chromosphere and differences in propagation between cases with waves interpreted to be resonant or nonresonant with the overlying coronal structures. This establishes the wave connection to coronal element abundance anomalies through the action of the wave ponderomotive force on the chromospheric plasma, which interacts with chromospheric ions but not neutrals, thereby providing a novel mechanism of ion-neutral separation. This is seen as a “First Ionization Potential Effect” when this plasma is lifted into the corona, with implications elsewhere on the Sun for the origin of the slow speed solar wind and its elemental composition.